title: Peritoneal metastasis 44

value: CRC

value: peritoneal metastasis


title: C.UT2

status: Public on May 01 2024

type: SRA

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

country: USA

institute: University of Illinois at Urbana-Champaign

library_source: transcriptomic

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p14 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (≥|2.0|-fold and ≤5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Assembly: human genome assembly NCBI GRCh38.p14
Supplementary files format and content: TMM normalized log counts per million (log CPM) values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: testes

growth_protocol: Cells were plated in DMEM with 10% FBS and 1% L-glutamine and 1x-Antibiotic/antimycotic

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.

treatment_protocol: (cells) indicated PFOS or vehicle control for 4 days; (mice) dosed with indicated PFAS or vehicle control for 15 days

tag: strain

tag: tissue

value: testes

tag: cell line

value: normal testes

tag: treatment

value: control


title: Peritoneal metastasis 43

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

data_processing:
Alignment protocol to be described
Read counts were normalized to log transformed transcript per million (TPM) values
Assembly: GRCh38
Supplementary files format and content: tab delimited file containing count values for all samples
Supplementary files format and content: tab delimited file containing tpm values for all samples

organism: Homo sapiens

source_name: peritoneal metastasis

extract_protocol:
RNA  was harvested from FFPE samples using the Qiagen AllPrep DNA/RNA Mini Kit following the manufacturer protocol
Library construction protocol to be described

tag: disease state


title: [Liver] [Ethanol-fed + Vehicle] [Replicate 1]

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Sequencing was performed on an Illumina NextSeq 2000
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the GRCm39 reference assembly using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using GRCm39.106.gtf.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file of HTSeq raw counts

source_name: Liver

extract_protocol:
Total RNA was extracted using the standard RNA-STAT60 and chloroform method. Samples were then treated with DNase, Amplification Grade I to digest single- and double-stranded DNA species. Finally, RNA samples were treated with RNAClean XP beads at a 1:1 volume ratio to further purify our samples to remove salts, dNTPs, and miscellaneous enzymes
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used for library construction

treatment_protocol: Male C57BL/6J mice were exposed to 0.2 mg/kg PCB126 or corn oil vehicle prior to ethanol feeding in the chronic-binge model.

value: Liver

tag: Sex

value: male

tag: diet

value: EtOH

tag: agent

value: Vehicle


title: Peritoneal metastasis 42


title: NPA+aKG, H3K4me3, ChIP

city: La Jolla

first: Mannix

last: Burns

email: mburns@salk.edu, mannixburns@gmail.com

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

library_source: genomic

data_processing:
Reads were aligned to the mm10 genome using the STAR alignment tool (version 2.5.3).
Peaks were called against an input control using MACS2 callpeak with the default --broad settings
BigWig files were subsequently generated using the HOMER makeBigWig command.
Assembly: mm10
Supplementary files format and content: bw
Supplementary files format and content: peak files (except input)

molecule: genomic DNA

extract_protocol:
Cells were crosslinked with 1% paraformaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 min. Quenched cells were washed twice with ice-cold PBS supplemented with protease inhibitors (Cell Signaling Technology). Cell pellets were mixed with provided buffers to isolate the nuclei which were then treated with 1-2 μl of micrococcal nuclease for 30 min at 37°C to digest DNA to the length of approximately 150-1000 bps followed by sonication with a focused ultrasonicator (Covaris).
Isolated ChIP DNA was library prepped using the NEBNext Ultra II DNA Library Prep Kit for Illumina in accordance with the manufacturer’s protocol

tag: cell type

value: mouse melanoma cell line

tag: chip antibody

value: 3-NPA + aKG


title: Testes, cKO-3, Day 9

city: China

first: hongwei

last: Wei

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

country: China

institute: South China University of Technology

data_processing:
StringTie v1.3.1
For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software
Assembly: Ensembl_release106
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Testes

extract_protocol:
The RNeasy micro-RNA isolation kit (Qiagen, Valencia, CA, USA) was used to isolate and purify total RNA from the testes. 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

value: Testes

tag: genotype

value: conditional Dcaf2 knockout


title: NPA, H3K4me3, ChIP


title: DMSO, H3K4me3, ChIP

value: DMSO


title: C.UT1


title: Peritoneal metastasis 41


title: [Liver] [Pair-fed + PCB 126] [Replicate 5]

value: pair-fed


title: [Liver] [Pair-fed + PCB 126] [Replicate 6]


title: Peritoneal metastasis 45


title: Peritoneal metastasis 40


title: [Liver] [Pair-fed + PCB 126] [Replicate 4]


title: NPA+aKG, input, ChIP


title: Testes, cKO-2, Day 9


title: Testes, cKO-1, Day 9


title: [Liver] [Pair-fed + PCB 126] [Replicate 3]


title: Peritoneal metastasis 38


title: NPA, input, ChIP


title: Testes, Control-2, Day 9


title: Peritoneal metastasis 39


title: [Liver] [Pair-fed + PCB 126] [Replicate 2]


title: Testes, Control-3, Day 9


title: [Liver] [Pair-fed + PCB 126] [Replicate 1]


title: Peritoneal metastasis 37


title: TA muscle of aging mice, SELENOW knockout, K3

city: wuhan

first: JiaCheng

last: Yang

address: Huazhong agriculture university

department: State Key Laboratory of Agricultural Microbiology

institute: HuaZhong Agricultre university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastpv23.0
Trimmed sequence reads were mapped to GRCm39. using hisat2
Read count extraction and normalization were performed with R
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Counts values for each Sample

source_name: Skeletal muscle

growth_protocol: Mice were caged in groups (5/cage) located in a room at 22 ± 2 ◦C and with a 12 h light/dark cycle, given free access to diet and water, and checked daily.

extract_protocol:
2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®   following manufacturer's protocols.

treatment_protocol: young mice rasing until mice were 24-month-old

value: Skeletal muscle

value: SELENOW knockout

value: natural aging, 24month-old


title: Testes, Control-1, Day 9


title: TA muscle of aging mice, SELENOW knockout, K2


title: [Liver] [Pair-fed + Vehicle] [Replicate 6]


title: Peritoneal metastasis 36

value: CRC

value: peritoneal metastasis


title: TA muscle of aging mice, SELENOW knockout, K1


title: Con

city: Seoul

first: Jeongbin

last: Park

state: Not US or Canada

address: 23, Sinhyeon-ro 38beon-gil, Siheung-si, Gyeonggi-do, 14957, Rep. of KOREA

department: Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea

country: South Korea

institute: Seoul National University

description: Fresh frozen Spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
We used spaceranger mkref in Space Ranger (version 2.0.1) pipeline to combine the human reference, GRCh38, with the mouse reference, mm10.
We ran spaceranger count on each sample to generate the processed ST cDNA library against a combined human and mouse reference genome to detect human transcripts from the administered cells in mouse tissues, if any.
Assembly: GRCh38 and mm10
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Lung Fibrosis

growth_protocol: Normal bone marrow derived hMSC was prepared from Lonza™. We prepared five male C57BL/6 mice, each 9 weeks old. The first class was a normal mouse (labeled ‘Nor’). The second class was two mice with lung fibrosis, serving as a control (labeled ‘Con’ or ‘Con-2’). The third class was two mice with lung fibrosis, but they also received an injection of hMSC through their tail veins, making them the experimental group (labeled ‘Exp’ or ‘Exp-2’). Lung fibrosis was triggered in both the control (‘Con’ or ‘Con-2’) and experimental (‘Exp’ or ‘Exp-2’) groups by injecting bleomycin for 3 weeks before they were sacrificed.

extract_protocol:
Optimal cutting temperature (OCT) blocks (Scigen 4586, USA) were made according to the Visium Spatial Protocols – Tissue Preparation Guide (Document CG000240). The OCT blocks from the experimental group were created 6 hours after injecting human stem cells. For each sample of all the classes, two tissue slices were acquired from each OCT mold. One was prepared for H&E staining, and the other was kept as a fresh frozen slice for Visium ST library.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer’s construction.

treatment_protocol: Bone marrow-derived hMSC was injected intravenously into the ‘Exp’ and ‘Exp-2’ samples, which were then sacrificed 6 hours later.

value: Lung Fibrosis


title: [Liver] [Pair-fed + Vehicle] [Replicate 4]


title: TA muscle of aging mice, wildtype, W3

value: WT


title: Con-2


title: Peritoneal metastasis 35


title: Peritoneal metastasis 34


title: [Liver] [Pair-fed + Vehicle] [Replicate 3]

value: Liver


title: DMSO, input, ChIP


title: Peritoneal metastasis 33


title: Nor

source_name: Normal Lung

value: Normal Lung


title: TA muscle of aging mice, wildtype, W2


title: Peritoneal metastasis 32


title: WT3 Input

city: Chicago

last: Kahl

address: 303 E Superior St

institute: Northwestern University

data_processing:
STAR was used for read alignments. exomePeak was used for peak calling. MemeChip was used for motif analysis. Ontology was performed with DAVID. Meta-analysis was performed using MetaPlot.
Assembly: GRCm38
Supplementary files format and content: Consistent Peaks across replicates are presented as .bed files for the WT and KO. Genes for each peak are listed with peak coordinates as well.

molecule: polyA RNA

source_name: Cortex/Hippocampus

growth_protocol: DMEM/F12 + B27/N2/Glutamine. Cultured at 37C and 5% CO2

extract_protocol:
RNA was extracted using Trizol and submitted to library building. m6A-IP samples were subjected to immunoprecipitation using an anti-m6A antibody prior to library building.
Libraries were built using the Illumina TruSeq Stranded mRNA Library Prep Kit.

value: Cortex/Hippocampus

value: Input


title: TA muscle of aging mice, wildtype, W1


title: [Liver] [Pair-fed + Vehicle] [Replicate 1]

value: male

value: Vehicle


title: ko_4d_RNAseq_rep2

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Paired-end 150 bp reads of RNA-seq data were aligned to mm9 genome reference (UCSC) using STAR alignment tool (version 2.7.3a) . Uniquely mapped reads were employed to quantify gene expression using RSEM software (version 1.3.1) . Transcripts per million mapped reads (TPM) were calculated to estimate the gene expression levels, normalized for sequencing depth. Euclidean distance based on TPM values were used to evaluate the similarities across biological replicates. Differential gene expression (DGE) analysis was performed using DESeq2 R package
Raw reads of ATAC-seq data were trimmed  using TrimGalore (version 0.6.1). Trimmed reads were aligned to mm9 genome reference (UCSC) using Bowtie2 aligner.uniquely mapped reads were employed to carry out peak calling using MACS2. Genomic distribution of ATAC peaks was annotated by “ChIPseeker” R package
The CUT&Tag reads were aligned to the mm10 genome by using Bowtie2. Low-mapping-quality reads were filtered by SAMtools (v.1.9), and duplicate reads were removed by Picard tools (v1.90).MACS2 (41) was used to call  peaks with a q-value < 0.01. BigWig files were generated by deeptools (46) by theRPKM normalization method and visualized in igv (v.2.13.1)
Assembly: mm9，mm10

source_name: bone-marrow-derived macrophage

extract_protocol:
Total RNA was extracted using Trizol reagent kit(Invitrogen). Total RNA transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530)
Genomic DNA was extracted after tagementation of Tn5 transposome. Barcoded libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
Genomic DNA was extracted after tagementation of PAG-Tn5 and the libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)
Total RNA transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530)
ATAC-seq libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
CUT&Tag libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)
RNA-seq; ATAC-seq; CUT&Tag

value: bone-marrow-derived macrophage

value: Arid1a Knock out

value: Osteoclastic differentiation

tag: time

value: Day 4


title: Peritoneal metastasis 31


title: WT2 Input


title: Peritoneal metastasis 30


title: [Liver] [Pair-fed + Vehicle] [Replicate 2]

value: pair-fed


title: WT1 Input


title: PC1_rep3

city: Guangzhou

first: Yingying

last: Zhao

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

institute: Guangzhou Institutes of Biomedicine and Health

data_processing:
RNA-seq: Data quality control for raw data using FastQC (v0.11.4)
RNA-seq: Preprocessing of raw reads using cutadapt (version 2.6)
RNA-seq: Read aligned to the human reference genome using STAR (version 2.7.10a)
RNA-seq: Quantification of gene expression of RNA-seq using RSEM (v1.2.28)
scRNA-seq: Data quality control for raw data using FastQC (v0.11.4)
scRNA-seq: Read aligned to the human reference genome using STARsolo (version 2.7.10a)
scRNA-seq:The BAM files in the results of STARsolo were visualized using IGV(2.8.9)
Assembly: hg38
Supplementary files format and content: RNA-seq: tab-delimited table containing gene count values, TPM values, FPKM values
Supplementary files format and content: RNA-seq: tab-delimited table containing isoform count values, TPM values, FPKM values

extract_protocol:
RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction.
scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).
scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS).

value: SHANK2 Mutation


title: ko_4d_RNAseq_rep1


title: WT3 IP

value: m6A IP


title: Peritoneal metastasis 29

value: CRC


title: ko_2d_RNAseq_rep2

value: Day 2


title: [Liver] [Pair-fed + Vehicle] [Replicate 5]


title: PC1_rep2


title: ko_2d_RNAseq_rep1


title: WT2 IP


title: Peritoneal metastasis 28

value: peritoneal metastasis


title: WT1 IP

value: WT


title: HC1_rep3


title: ko_0d_RNAseq_rep2

value: Day 0


title: Peritoneal metastasis 27


title: Peritoneal metastasis 26


title: HC1_rep2


title: KO2 Input

value: Mettl14 KO


title: KO1 Input

value: Cortex/Hippocampus


title: HC1_rep1


title: Peritoneal metastasis 25


title: KO2 IP


title: Peritoneal metastasis 24


title: HUVEC, IFNg-3

city: St. Petersburg

first: JUNKO

last: SAWADA

address: 600 5th Street South

institute: Johns Hopkins All Children's Hispital

data_processing:
Read data was processed in BaseSpace (basespace.illumina.com). Reads were aligned to Homo sapiens genome (hg19) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Assembly: Reads were aligned to Homo sapiens genome (hg19) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Supplementary files format and content: fpkm

source_name: HUVEC

growth_protocol: HUVEC was maintained with EGM-2 medium

extract_protocol:
RNA was extracted by TRIzol
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).
Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA)

treatment_protocol: HUVEC cells were cultured at 2X10(5)/well in the 6-well plate. The next day, the cell medium was replaced with 10 ng/ml TNFa, 10 ng/ml IL-4, 50 ng/ml IFNg, or control (EGM-2 medium only) and cultured 2 days. RNA was isolated and used for the library generation.

value: HUVEC

value: endothelial cell

value: IFNg


title: wt_4d_RNAseq_rep1

value: bone-marrow-derived macrophage


title: Peritoneal metastasis 23


title: HUVEC, IFNg-2


title: RCaP_2

city: Cold Spring Harbor

first: Lloyd

last: Trotman

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE vM5 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample.

source_name: Epithelial cells

extract_protocol:
Total RNA was extracted using TRIzol
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

value: Pten and Trp53 deleted; prostate cancer cells


title: RCaP_1


title: PC1_rep1


title: wt_2d_RNAseq_rep1

value: Osteoclastic differentiation


title: Peritoneal metastasis 22


title: HUVEC, IFNg-1


title: wt_0d_RNAseq_rep2


title: HUVEC, IL4-3


title: Peritoneal metastasis 21


title: colon enterocytes [mouse] - [Epcam+, Cd44-neg, Cd66a-high] - [replicate #1]

city: Nutley

first: Piero

last: Dalerba

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation (CDI)

institute: Hackensack Meridian Health

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ003

data_processing:
RNA-seq data was processed and mapped using OLego (Wu et al., Nucleic Acids Research, 41:5149–5163, 2013) and normalized using standard computational pipelines such as cufflinks (Trapnell et al., Bioinformatics, 25:1105-1111, 2009; Trapnell et al., Nature Protocols, 7:562-578, 2012). Mapping was performed onto the UCSC mm10 mouse genome. Gene-expression levels were quantified by computing Transcripts per Million (TPM) values. Computation of gene-level TPM values and retriveal of gene annotations were performed using the tximport and biomaRt software packages, implemented within the R software. A custom PYTHON script was used to organize the data. Finally, gene-expression levels were reported either as log2(TPM) values (when TPM>1), or as (TPM-1) values (when TPM=1 or TPM<1).
Assembly: Genome assembly: UCSC mm10
Supplementary files format and content: Tab-delimited text files report expression levels for each gene in each sample. Gene-expression levels are reported either as log2(TPM) values (when TPM>1), or as (TPM-1) values (when TPM=1 or TPM<1).

source_name: colon epithelial cells [mouse]

growth_protocol: Colon epithelial cells were purified from primary colonic tissues of adult female mice (strain: C57BL/6J; source: The Jackson Laboratory, stock #000664).

extract_protocol:
Sorted cells were centrifuged to form a pellet and flash-frozen in liquid nitrogen. Total RNA was extracted using the NuceloSpin RNA XS kit (Macherey-Nagel).
RNA-seq libraries were generated using the Illumina Stranded mRNA Prep kit, which employes poly-A oligonucleotides in order to "pull-down" mRNAs. RNA-seq libraries were sequenced using either an Illumina HiSeq 4000 machine (30 million, single-end, 100 bp reads) or an Illumina NovaSeq 6000 machine (20 million, paired-end, 100 bp reads). Individual samples are annotated with regard to the platform used to sequence them.

treatment_protocol: Whole epithelial crypts were detached from colon tissues using EDTA (5 mM) and then dissociated into single-cell suspensions using DNAse-I (100 units/ml) and Collagenase-III (200 units/ml). Single-cell suspensions were stained first with monoclonal antibodies (anti-Epcam FITC, clone G8.8, BioLegend; anti-Cd44-APC, clone IM7; BioLegend; anti-Kit-PE, clone 2B8, BioLegend; anti-Cd66a-APC/Cy7, clone Mab-CC1, BioLegend; anti-Cd3-PE/Cy5, clone 17A2, BD Biosciences; anti-Cd16/Cd32-biotin, clone 2.4G2, BD Biosciences; anti-Cd31-biotin, clone 390, eBioscience; anti-Cd45-biotin, clone 30F-11, BD Biosciences) and secondarily with Streptavidin-PE/Cy5 (BD Biosciences). Target epithelial populations (Epcam+/Cd44+/Kit-neg, Epcam+/Cd44+/Kit+, Epcam+/Cd44-neg/Cd66a-high) were sorted by FACS, after exclusion of dead cells (DAPI+), cell doublets (serial gating based on FSC-A vs. FSC-H and SSC-A vs. SSC-W profiles) and cells of non-epithelial lineages (Cd3+, Cd16/Cd32+, Cd31+, Cd45+), as previously published (Rothenberg et al., Gastroenterology, 142:1195-1205, 2012).

value: female

tag: cell phenotype

value: Epcam+, Cd44-neg, Cd66a-high

value: enriched in enterocytes [top crypt]


title: wt_0d_RNAseq_rep1


title: ko_0d_RNAseq_rep1

value: Arid1a Knock out


title: HUVEC, IL4-2


title: Peritoneal metastasis 20

value: CRC


title: wt_4d_RNAseq_rep2

value: Day 4


title: Peritoneal metastasis 19

value: peritoneal metastasis


title: HUVEC, IL4-1


title: colon Lgr5+ cells [mouse] - [Epcam+, Cd44+, Kit-neg] - [replicate #1]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ002

value: Epcam+, Cd44+, Kit-neg

value: enriched in Lgr5+ cells [bottom crypt]


title: colon goblet cells [mouse] - [Epcam+, Cd44+, Kit+] - [replicate #1]

description:
C57BL/6J - The Jackson Laboratory [stock #000664]
PJ001

value: Epcam+, Cd44+, Kit+

value: enriched in goblet cells [bottom crypt]


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E9.5, 2

city: New York

first: Arielle

last: Strasser

address: 1425 Madison Ave

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Preprocessing of 10X Genomics scRNA-seq data, clustering, and cell type identification was performed using Cellranger software version 7.0.0.
Filtered gene and barcode count matrices were used for scRNA-seq analysis with a custom R pipeline built with the Seurat package v4.0.0 86,87, in addition to other publicly available R toolkits.
Assembly: mm10-3.0.0, customized to include Cre recombinase sequence
Supplementary files format and content: CellRanger filtered gene matricies

source_name: Forelimb buds

extract_protocol:
Dissections were performed under a stereomicroscope in multiple changes of cold phosphate-buffered saline (PBS). Limb buds were digested at 37 °C in 0.5 mL of 0.25% trypsin/EDTA (Invitrogen, 25200-072) for 5 minutes at 37°C with trituration by pipetting at 2.5 and 5 minutes. Trypsinization was stopped by adding 0.5 mL of cell culture medium DMEM (CO & CAT #) with 10% FBS (CO & CAT #). Cell suspensions were centrifuged at 300g and 4 °C for 3 minutes. Supernatant was removed, and cells were resuspended in 0.5 mL of pre-chilled (4 °C) 10% DMSO in FBS. Cell suspensions were then transferred into cryovials, placed into a pre-chilled freezing container (CO & CAT #) at -80°C overnight, and transferred to -150°C for long term storage the following day. Once sufficient samples were generated, cryovials were thawed at 37 °C and transferred into a 15 mL centrifuge tube. 1 mL of pre-warmed (37 °C) cell culture medium was added dropwise with gentle tube shaking, followed by an additional 2 mL of medium. Three samples were then pooled into one 15 mL centrifuge tube and mixed well prior pelleting at 300 g for 3 minutes. The media was then aspirated slowly leaving approximately 50 µl of supernatant and cells were resuspended in 1 mL of freshly made 0.04% BSA in PBS. Cell suspensions were then strained through a 40 μm filter (Falcon, 352340), pelleted at 300g for 3 minutes, aspirated to approximately 50 µl of supernatant, and resuspended in 50 uL of 0.04% BSA in PBS.
scRNA-seq 3' expression libraries were prepared on a Chromium instrument (10X Genomics, model  GCG-SR-1) using the Chromium Single Cell Gene Expression kit (version 3).

value: Mesenchymal limb buds

value: Forelimb buds

tag: age


title: KO1 IP

value: Cortex/Hippocampus

value: Mettl14 KO

value: m6A IP


title: HUVEC,LTa1b2-3

value: HUVEC

value: endothelial cell


title: wt_2d_RNAseq_rep2

value: bone-marrow-derived macrophage

value: WT

value: Osteoclastic differentiation

value: Day 2


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E9.5, 1

description: 10x Genomics


title: S963Nr24: GM-CSF WT (Cre-) heat fixed S. aureus Rep3

city: Freiburg

first: Aaron

middle: James

last: Forde

address: Breisacher Str. 115

country: Germany

institute: Medical Center University of Freiburg

data_processing:
De-multiplexing: Illumina bcl2fastq
Trimming: Skewer (V0.2.2)
Read count: STAR (V2.5.2b)
Quality control reads: FASTQC
Alignment: STAR (V2.5.2b)
Differentially expressed genes: DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab seperated values-files of raw_reads, normalized_reads and differentially expressed genes (fold change and adjusted p-values) comparing infected vs control BMDM and infected vs bystanding BMDM

source_name: Bone marrow-derived macrophages

growth_protocol: Murine bone marrow was cultured in RPMI with 10% fetal calve serum, 0,5% ciprofloxacin and M-CSF (20ng/ml) or GM-CSF (20ng/ml) for 6 days. After 6 days the BMDMs were harvested and underwent cell sorting. M-CSF BMDMs were sorted based on being double poisitve for CD11b and F4/80. GM-CSF BMDMs were sorted based on high CD115 expression and negative for MHCII

extract_protocol:
100ng of total RNA, obtained with QIAGEN microkit, was subjected to library synthesis using the TruSeq Stranded  mRNA Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following sorting the macrophages were allowed to adhere overnight. The BMDMs were either left untreated (control) or stimulted with with heat fixed S. aureus for 4 hours

value: LysMcre/+::HIF1{alpha}fl/fl (Cre-)

value: Bone marrow-derived macrophages

value: GM-CSF (20ng/ml) for 6 days

value: stimulated for 4 hours with heat fixed S. aureus


title: Esco2fl/fl, control, E9.5

description: 10x Genomics


title: Peritoneal metastasis 17

value: CRC

value: peritoneal metastasis


title: S963Nr23: GM-CSF WT (Cre-) heat fixed S. aureus Rep2


title: HUVEC,LTa1b2-1


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E11.5, replicate 3

data_processing:
Illumina data were processed through Illumina’s Real-Time Analysis (RTA) software generating base calls and corresponding base call quality scores.
CIDRSeqSuite 7.1.0 was used to convert compressed bcl files into compressed fastq files.
RNA-sequencing data was subjected to adapter removal with cutadapt.
Paired-end reads were then mapped to the mouse (mm10) reference genome using STAR and gene count summaries were generated using featureCounts.
Raw fragment (i.e. paired-end read) counts were then combined into a numerical matrix, with genes in rows and experiments in columns, and used as input for differential gene expression analysis with the Bioconductor Limma package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing genes and counts

source_name: forelimb limb bud cells

extract_protocol:
Individual limb buds were isolated and purified using Qiagen’s RNeasy Micro Kit (Qiagen: 74004). High quality RNA with RIN scores >9.5 were selected for library preparation.
Library preparation was performused using the NEBNext® UltraIITM DNA Library Prep Kit for Illumina (NEB #E7103).

value: forelimb limb bud cells

tag: developmental stage


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E11.5, replicate 2


title: Peritoneal metastasis 16


title: HUVEC, TNFa3

value: TNFa


title: S963Nr22: GM-CSF WT (Cre-) heat fixed S. aureus Rep1


title: S963Nr21: GM-CSF HIF1α ko (Cre+) heat fixed S. aureus Rep3

value: LysMcre/+::HIF1{alpha}fl/fl (Cre+)


title: HUVEC, TNFa2


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E11.5, replicate 1


title: S963Nr20: GM-CSF HIF1α ko (Cre+) heat fixed S. aureus Rep2


title: Peritoneal metastasis 14


title: Peritoneal metastasis 13


title: S963Nr19: GM-CSF HIF1α ko (Cre+) heat fixed S. aureus Rep1


title: Peritoneal metastasis 18


title: HUVEC, TNFa1


title: Peritoneal metastasis 12


title: HUVEC,  control3

value: Control


title: HUVEC,LTa1b2-2


title: HUVEC,  control2


title: S963Nr18: GM-CSF WT (Cre-) Control Rep3

value: untreated (control)


title: Peritoneal metastasis 11


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E9.5, replicate 3


title: Peritoneal metastasis 15


title: Peritoneal metastasis 10


title: Peritoneal metastasis 09


title: S963Nr16: GM-CSF WT (Cre-) Control Rep1


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E9.5, replicate 2


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E9.5, replicate 1


title: HUDEP-2 WT DNase-I 60U/mL

city: Seattle

first: Jeff

last: Vierstra

state: WA

address: 2211 Elliot Ave

institute: Altius Institute for Biomedical Sciences

data_processing:
Basecalling, RTA v3.4.4
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.3
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Assembly: GRCh38
Supplementary files format and content: Normalized DNaseI density bigWig files
Library strategy: DNaseI-seq

growth_protocol: HUDEP-2 were maintained in Iscove's modified Dulbecco's medium (IMDM) supplemented with 330 μg/mL human holo-transferrin (Sigma), 10 μg/mL recombinant human insulin (Sigma), 2 IU/mL heparin (Sigma), 5% human AB plasma (obtained from Bloodworks Northwest, Seattle, WA), 3 IU/mL EPO, 100 ng/mL SCF, 1 μg/mL doxycycline (Sigma), and 100 units/ml penicillin/streptomycin.

extract_protocol:
Nuclei from 100,000-200,000 cells were extracted in the presence of 0.04% de-ionized IGEPAL CA-630 incubated at 4 ºC for 10 min. Nuclei were treated with a gradient of DNase I solution (40 IU to 100 IU of DNase I) for 3 min at 37 ºC. DNase I digestion was quenched by adding an equal volume of 5X Stop buffer and 20μL RNase A (Sigma, R4642) followed by incubation at 37 ºC for 60min. After incubation, 1μL of Proteinase K (Sigma, P4850) was added and the reactions were incubated at 50 ºC for 60min. Digested genomic DNA was visualized on 1.2% agarose gen and the fragment size profile was generated using the Fragment Analyzer (Advanced Analytical). Prior to genomic library generation, fragments were subjected to size selection with large fragment depletion by magnetic bead separation. Fragment size distribution and concentration of the fractionated sample was measured with Fragment Analyzer (Advanced Analytical).
Illumina compatible, double-stranded DNA library libraries from the size fractionated samples were constructed using the ThruPLEX DNA-seq Kit (Takara Bio) according to manufacturer’s instructions.

value: human erythroid progenitors

value: untreated


title: S963Nr15: GM-CSF HIF1α ko (Cre+) Control Rep3


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E10.5, replicate 3


title: HUDEP2 WT GATA1 CUT&RUN

data_processing:
Basecalling, RTA v3.4.4
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.3
Read density, Bedops v2.4.19
Assembly: GRCh38
Supplementary files format and content: Normalized H3K27ac CUT&RUN density bigWig file
Supplementary files format and content: Normalized GATA1 CUT&RUN density bigWig file
Library strategy: CUT&RUN

extract_protocol:
After immobilization of 2x10E5 HUDEP-2 cells with Concannavalin A-coated beads DNA was extracted using phenol-chloroform, iso-amly alcohol precipitation
Illumina compatible, double-stranded DNA library libraries from the size fractionated samples were constructed using the ThruPLEX DNA-seq Kit (Takara Bio) according to manufacturer’s instructions.


title: PFOS_5mg.3

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p14 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (≥|2.0|-fold and ≤5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Assembly: human genome assembly NCBI GRCh38.p14
Supplementary files format and content: TMM normalized log counts per million (log CPM) values for each Sample

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.

value: testes

value: normal testes

value: 5 mg/kg PFOS


title: Esco2fl/fl, control, E11.5, replicate 3


title: HUDEP2 WT H3K27ac CUT&RUN

value: WT


title: S963Nr14: GM-CSF HIF1α ko (Cre+) Control Rep2


title: Peritoneal metastasis 08

data_processing:
Alignment protocol to be described
Read counts were normalized to log transformed transcript per million (TPM) values
Assembly: GRCh38
Supplementary files format and content: tab delimited file containing count values for all samples
Supplementary files format and content: tab delimited file containing tpm values for all samples

extract_protocol:
RNA  was harvested from FFPE samples using the Qiagen AllPrep DNA/RNA Mini Kit following the manufacturer protocol
Library construction protocol to be described


title: Peritoneal metastasis 07


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E10.5, replicate 1


title: S963Nr13: GM-CSF HIF1α ko (Cre+) Control Rep1


title: LnCap BG4 ChIP-seq rep4

city: Xi'an

first: Yue

last: Hou

state: Shaanxi

address: No.28, West Xianning Road, Xi'an, Shaanxi, 710049,P.R. China

institute: Xi'an JiaoTong University

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After removing adaptor sequences, the reads were mapped to the reference human genome (hg19) with bowtie v2.2.5 with the default parameters
Unmapped reads, non-uniquely mapped reads, reads with mapping quality below ten or marked as duplicates were removed by using samtools v1.11
MACS2 v2.1.1 was used to identify peaks with a cutoff p-value of 0.01
Assembly: hg19
Supplementary files format and content: narrowPeak files

source_name: LnCap

growth_protocol: LnCap cells were  cultured  at  378C  in  a  humidifiedenvironment of 5% CO2in air, and the medium wasreplenished twice weekly.

extract_protocol:
Chromatin was isolated from LnCap cells that were cross-linked using 1% formaldehyde. Chromatin was sonicated using a Bioruptor Plus to give a fragment distribution of 100-500 bp. For further details see methods section in the associated manuscript.
BG4 ChIP-seq was modified from a previously published protocol (Hansel-Hertsch et al., 2018).

value: LnCap

value: Prostate cancer cell lines


title: S963Nr12: M-CSF WT (Cre-) heat fixed S. aureus Rep3

value: LysMcre/+::HIF1{alpha}fl/fl (Cre-)

value: Bone marrow-derived macrophages

value: M-CSF (20ng/ml) for 6 days


title: Esco2fl/fl;Prrx1-CreTg/0, mutant, E10.5, replicate 2


title: S963Nr17: GM-CSF WT (Cre-) Control Rep2

value: GM-CSF (20ng/ml) for 6 days


title: Peritoneal metastasis 05

value: CRC

value: peritoneal metastasis


title: Peritoneal metastasis 06


title: Esco2fl/fl, control, E11.5, replicate 1

value: forelimb limb bud cells


title: Esco2fl/fl, control, E11.5, replicate 2


title: HUVEC,  control1

value: HUVEC

value: endothelial cell

value: Control


title: S963Nr11: M-CSF WT (Cre-) heat fixed S. aureus Rep2

value: stimulated for 4 hours with heat fixed S. aureus


title: LnCap BG4 ChIP-seq rep3


title: Peritoneal metastasis 04


title: LnCap BG4 ChIP-seq rep2


title: Esco2fl/fl, control, E10.5, replicate 3


title: Peritoneal metastasis 03


title: Esco2fl/fl, control, E10.5, replicate 2


title: S963Nr10: M-CSF WT (Cre-) heat fixed S. aureus Rep1


title: S963Nr9: M-CSF HIF1α ko (Cre+) heat fixed S. aureus Rep3

value: LysMcre/+::HIF1{alpha}fl/fl (Cre+)


title: Esco2fl/fl, control, E10.5, replicate 1


title: S963Nr7: M-CSF HIF1α ko (Cre+) heat fixed S. aureus Rep1


title: LnCap BG4 ChIP-seq rep1


title: Peritoneal metastasis 02


title: Esco2fl/fl, control, E9.5, replicate 3


title: Tuft cells from human embryonic intestine [HUB-JO-s058]

city: Utrecht

first: Amir

last: Giladi

address: Uppsalalaan 8

institute: Hubrecht Institute

description: metadata.txt

data_processing:
STAR (version 2.7.8a)
Reads were demultiplexed and collapsed into UMI tables using umi_tools (version 1.1.1) allowing up to one hamming distance of the cell barcode. Cells with less than 500 UMI, or with more than 40% mitochondrial genes were excluded from analysis.
Assembly: hg38
Supplementary files format and content: Genes x cells tab delimited table
Supplementary files format and content: A metadata file containing relevant information (experiment condition, etc.) for each sequenced cell
Supplementary files format and content: Matrix file containing number of detected transcripts per feature and cell
Supplementary files format and content: A features file (either gene or Cellplex barcode)
Supplementary files format and content: A barcodes (cells) file

source_name: Cells A1-E1 colon, cells E2-H24,N1-N20,O1-P24 Ileum, cells I1-K24 Jejunum, cells M1-M24,N21-N24 Duodenum

growth_protocol: Human intestinal organoids were split once a week by mechanic dissociation. In this study, basic culture medium includes advanced Dulbecco’s modified Eagle’s medium/F12 (Gibco) supplemented with 100 U/ml penicillin/streptomycin (Gibco), 10 mM HEPES (Gibco), 1× Glutamax (Gibco), 1× B-27 Supplement (Life Technologies), 1.25 mM N-acetylcysteine (Sigma-Aldrich) and 1% (v/v) recombinant Noggin (U-Protein Express).

extract_protocol:
Single cell samples were lysed, barcoded and processed according to the CEL-Seq2 technique. Cells were sorted into 384 well plates, containing UMI barcode primers, frozen and incubated at 65°C for 5min to ensure lysis. First and second strand synthesis (Invitrogen) was performed and all wells of a single plate were pooled. Afterinvitrotranscription (Ambion), the amplified RNA was reverse transcribed and amplified for 10-12 cycles with Illumina Truseq primers.
Organoids were dissociated into single cells using TrypLE (TrypLE Express, Life Technologies) with 10 μM Rho kinase inhibitor (Abmole) in 37°C and mechanical disruption by pipetting every 5 minutes.

treatment_protocol: Organoids were expanded in human expansion medium as described before. For differentiation toward tuft cells, organoids were washed 30 minutes in DMEM+++ at day 4 and the medium is replaced for tuft cell differentiation medium (diff): 0.5 nM Wnt surrogate (U-Protein Express), 20% (v/v) R-spondin1 (condition medium), 50 ng/ml recombinant human EGF (Peprotech), 10 μM Notch inhibitor DAPT (Sigma-Aldrich) in basic culture medium. For tuft cell differentiation with IL-4 and IL-13, EGF was withdrawn, 5 ng/ml human IL-4 (Peprotech) and 5 ng/ml human IL-13 (Peprotech) were supplemented to tuft cell differentiation medium (diff).

value: Cells A1-B24 EPCAM+ epithelial cells, rest KIT+ tuft cells

tag: patient age

value: fetal


title: Peritoneal metastasis 01

city: Amsterdam

last: van Hooff

address: Meibergdreef 9

institute: AUMC


title: LnCap BG4 ChIP-seq input


title: AVIL+ tuft cells from Ileal human organoids [HUB-JO-s057]

description: metadata.txt

source_name: Ileum

value: Ileum

value: Ileum-derived organoids

value: AVIL+ tuft cells

value: AVIL-Clover genetic tag

value: Differentiation medium with IL-4/IL-13 supplementation

value: adult


title: S963Nr6: M-CSF WT (Cre-) Control Rep3

value: LysMcre/+::HIF1{alpha}fl/fl (Cre-)

value: Bone marrow-derived macrophages

value: M-CSF (20ng/ml) for 6 days

value: untreated (control)


title: S963Nr8: M-CSF HIF1α ko (Cre+) heat fixed S. aureus Rep2


title: Tuft cells from human colon [HUB-JO-s054]

description: metadata.txt

source_name: Colon

value: Colon

value: KIT+ tuft cells


title: Parasrampuria_Round 4 NT

city: Winston-Salem

first: Keith

middle: T.

last: Gagnon

state: North Carolina

address: 575 Patterson Ave

department: Biochemistry and Molecular Biology

institute: Wake Forest University School of Medicine

data_processing:
Adapters trimmed from sequencing facility
Fastq files filtered using Trimmomatic (v0.39) to eliminate reads shorter than 15 nucleotides.
Filtered files were aligned to relevant reference small RNA fasta sequences using Bowtie (v1.2.2) and .sam files output.
.sam files analyzed in Tablet (v1.21.02.08) and exported as .txt files containing read coordinates in reference to aligned reference fasta.
An in house excel program used to analyze .txt files and reconstruct reads based on coordinates and reference nucleotide sequence. See supplementary file Tablet_Excel_Analysis.
Expression profiling was run on the fastq files using the online sRNAtoolbox software.
Supplementary files format and content: Excel spreadsheet analyzing the .txt Tablet files including processing precision of the designed small RNA.
Supplementary files format and content: Text files containing expression profiling results of the top ten microRNA per sample used to analyze endogenous miRNA knockdown between samples and NT controls.

source_name: HEK 293T

growth_protocol: HEK 293T cells were maintained in DMEM supplemented with 5% fetal bovine serum (FBS), 5% cosmic calf serum (CCS), and 1% non-essential amino acids (NEAA) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were harvested by trypsinization, and RNA was extracted using the mirVana miRNA Isolation Kit (Invitrogen) according to the manufacturer’s protocol.
Small RNA libraries were prepared using the Qiagen QiaSeq miRNA Library Prep kit and sequenced on an Illumina NovaSeq6000 with 76 cycles.

treatment_protocol: Small RNA expression vectors (875 ng) were electroporated into 350,000 HEK 293T cells using the Neon Transfection System (Invitrogen).

value: HEK 293T

value: WT

value: Transient transfection no treatment (NT) control


title: Esco2fl/fl, control, E9.5, replicate 2

value: forelimb limb bud cells


title: S963Nr5: M-CSF WT (Cre-) Control Rep2


title: AVIL- epithelial cells from Ileal human organoids [HUB-JO-s043]

description: metadata.txt

source_name: Ileum-derived organoids

value: AVIL- epithelial cells


title: S963Nr4: M-CSF WT (Cre-) Control Rep1


title: Parasrampuria_Round 3 NT


title: AVIL- epithelial cells from Ileal human organoids [HUB-JO-s042]

description: metadata.txt

value: Differentiation medium


title: WT_M1_Rep2

city: Wuhan

first: Chen

last: zhang

state: Hubei

address: Jiefang road 1037

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  subjunc (subread v2.0.1) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts (subread v2.0.1) with mouse annotation (release_M20) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.30.1) package of the R (version 4.0.4) software
Assembly: mm10
Supplementary files format and content: Comma-Separated Row counts for each sample

source_name: bone marrow

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 10 million cells were added with Trizol and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on NovaSeq 6000 platform .

value: bone marrow

value: macrophages

value: LPS+INFγ stimulated


title: S963Nr3: M-CSF HIF1α ko (Cre+) Control Rep3

value: LysMcre/+::HIF1{alpha}fl/fl (Cre+)


title: WT_M1_Rep1


title: Parasrampuria_shHD2.4

value: Transient transfection of smRNA encoding lentiviral plasmid


title: AVIL+ tuft cells from Ileal human organoids [HUB-JO-s037]

description: metadata.txt

value: Ileum-derived organoids

value: AVIL+ tuft cells

value: AVIL-Clover genetic tag

value: Cells 1-264 and 284 grown in differentiation medium (Diff), cells 265-286,288-384 grown in Diff with IL-4/IL-13 supplementation

value: adult


title: WT_M0_Rep1

value: unstimulated


title: Esco2fl/fl, control, E9.5, replicate 1


title: scRNA_LCMV_Day7_CD4_CD8_NK_KO

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

data_processing:
cDNA libraries were sequenced at ~500 million reads per sample with 50bp paired-end reads using NovaSeq (Illumina).
alignment: Sequencing reads were processed using Cell Ranger 3.0 (10x Genomics) to generate the FastQ files and cell counts. The matrix files generated from Cell Ranger were further analyzed using Seurat including quality control, filtering, normalization, scaling, clustering, visualization, differential expression analysis, cell population annotation. Gene Ontology (GO) analysis were performed using Enrichr and ggplot2 (https://ggplot2.tidyverse.org) in R. Downstream analyses were performed with custom R programs (http://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: .h5 files for single cell RNA-seq

source_name: CD4+CD8+NK cells

extract_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by  washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10  ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Single cell suspensions were sorted using a FACS Aria Fusion (BD). ~15K cells at a concentration of 800 cells/μl were processed using the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #1000121), the Chromium Next GEM Chip G Single Cell Kit (10x Genomics, #1000120) and the Chromium Controller (10x Genomics, #1000202). cDNA libraries were constructed using the Chromium Single Cell 3ʹ Library Kit (10x Genomics, #1000079) and Single Index Kit T Set A (10x Genomics, #1000213).

treatment_protocol:
Toxoplasma gondii infection protocol: Wild type and IfngCTCFdel mice were inoculated with an average of 15 cysts of type II avirulent T. gondii strain ME-49 by intraperitoneal injection
Toxoplasma gondii infection protocol: LCMV (strain Armstrong) was thawed at 37°C and then injected into mice by intraperitoneal injection at the concentration 2 x 10^5 plaque-forming units (PFU) per mouse.

value: Spleen

value: CD4+CD8+NK cells

tag: surface marker

value: CD4 (CD44+dump-CD4+), CD8 (CD44+dump-CD8+), NK (dump-NK1.1+NKp46+)

tag: culture condition

value: in vivo


title: Parasrampuria_shHD-33full_30lp2

value: HEK 293T

value: WT


title: S963Nr1: M-CSF HIF1α ko (Cre+) Control Rep1

tag: strain

value: Bone marrow-derived macrophages

value: M-CSF (20ng/ml) for 6 days

value: untreated (control)


title: Day 85 WA25

city: Boston

first: Karl

middle: Russell

last: Koehler

state: MA

address: 3 Blackfan Circle

department: Otolaryngology-Head and Neck Surgery

institute: Boston Children's Hospital-Harvard Medical School

data_processing:
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger wereused for further analysis.
Seurat 3.0.0.9000 was used for data normalization, data scaling, graph-based clustering, cluster marker genes identification.
Assembly: GRCh38

source_name: Skin Organoids

growth_protocol: Culture experiments were performed with the WA25 hESC line (passage 21-47), purchased from WiCell Research Institute, and the Desmoplakin-mEGFP (DSP-GFP) hiPSC line (passage 35-51), acquired from the Allen Institute for Cell Science and the Coriell Institute44. Cells were cultured on 6-well plates coated with Vitronectin Recombinant Human Protein (Invitrogen) at a concentration of 0.5 µg/cm2. Pluripotent stem cells were maintained in Essential 8 Flex (Gibco) medium with 100 µg/ml Normocin (hereafter, E8; Invivogen). The medium was replenished every other day. Cells were passaged at ~80% confluency (generally every 4-5 days) in medium containing 10 µM Y27632 (hereafter, Y; ROCK inhibitor that inhibits apoptosis, Stemgent). WA25 cells were passaged in clusters with 0.5 mM EDTA, and DSP-GFP cells were passaged as single cells with StemPro Accutase Cell Dissociation Reagent (hereafter, Accutase; Gibco). Fresh E8 medium was replenished twenty-four hours following passage. Detailed information concerning cell line specifics as well as validation and testing is available at: https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/wa25.cmsx?closable=true and https://www.allencell.org/cell-catalog.html.

extract_protocol:
To dissociate WA25 and DSP-GFP into single cells, randomly selected day-48 organoids (n = 6 per sample), day-85 organoids (n = 6 per sample), and day-133 organoids (n = 1 per sample) were dissociated and pooled (day 48/85) from each group. Briefly, collected organoids were incubated with pre-warmed (37°C) TrypLE™ for total 8-30 min (depending on the organoid sizes and densities) in a 37°C incubator on a shaker at 65 rpm for a gentle swirl. During the incubation, the dissociation mixture was agitated every 3-10 min with gentle pipetting using wide-bore p1000 and p200 tips (Mettler-Toledo). By total 8-30 min of incubation, the tissue structure dissociated into a single cell suspension with no visible cell aggregation. Cold 3% BSA solution (Sigma-Aldrich) was added to the dissociated cell suspension in order to inactivate TrypLE enzymatic activity. The suspension was filtered through a 40 µm Flowmi™ cell strainer (Bel-Art™) in order to eliminate any debris. An additional three washes with cold 3% BSA solution were performed. Cells were resuspended in 3% BSA, and filtered through a 40 µm Flowmi™ cell strainer. Viability (live cell percentage) and live cell count was determined using Trypan Blue (used at 1:1 ratio) and Countess II. Final cell concentration was ~1,000 cells/µl and >90% viability.
Single cell 3’ RNA-seq experiments were conducted using the Chromium single cell system (10x Genomics, Inc) and the NexSeq500 or NovaSeq 6000 sequencer (Illumina, Inc). Approximately 17,000 cells (targeting for 10, 000 cells) per sample were added to a single cell master mix, following the Chromium Single Cell 3’ Reagent Kits v2 User Guide, CG00052 Ver B (10x Genomics, Inc). Day-6 samples were processed using the Version 3 Chromium Single Cell 3’ Reagent Kits. Along with the single-cell gel beads and partitioning oil in separate wells of a Single Cell A Chip, the single cell reaction mixture was loaded to the Chromium Controller for GEM generation and barcoding, followed by cDNA synthesis and library preparation. At each step, the quality of cDNA and library was examined by Bioanalyzer. The resulting library was sequenced in a custom program for 26b plus 98b paired-end sequencing on an Illumina NextSeq500 or 28b plus 91b paired-end on Illumina NovaSeq 6000 to a read depth of >30,000 reads per cell.

treatment_protocol: For differentiation, pluripotent hPSC colonies were detached from the culture dish using Accutase. Once dissociated, hPSCs were collected as a single cell suspension in E8 medium containing 10 µM Y (hereafter, E8-10Y). Cell concentration was determined with an automated cell counter (Countess™ II Automated Cell Counter; Countess II, Life Technologies); Trypan blue (Gibco) was used at a ratio of 1:1 (Trypan blue:cell suspension) to distinguish dead vs. live cells. The appropriate number of live cells needed for an experiment was transferred into E8 medium containing 20 µM Y (hereafter, E8-20Y). From the E8-20Y cell suspension, cells were distributed at a count of 3,500 cells in 100 µl per well into 96-well U-bottom plates (Thermo Scientific). Aggregation was aided by centrifugation at 110 rcf for 6 min. These cell aggregates were incubated in 37°C incubator under 5% CO2 for 48 hrs. Thus, we designated this timepoint as day -2. After 24 hrs incubation (at day -1), fresh 100 µl E8 medium was added to each well in order to dilute out Y and promote cell proliferation and aggregate growth. On day-0, to start differentiation, all cell aggregates were individually collected and transferred to new 96-well U-bottom plates in 100 µl of E6-based differentiation medium containing 2% Matrigel (Corning), 10 µM SB (Stemgent), 4 ng/ml basic-FGF (hereafter, FGF2; PeproTech), and 2.5 ng/ml BMP-4 (PeproTech) to initiate non-neural ectoderm formation. On day-3 of differentiation, to induce CNCC formation, 200 ng/ml LDN (BMP inhibitor, Stemgent), and 50 µg/ml of FGF2 were added in a volume of 25 µl per well, thus making the final volume 125 µl per well. On day-6 of differentiation, 75 µl of fresh E6 medium was added, bringing the final volume to 200 µl. Half of the media was changed (removal of 100 µl spent medium and addition of 100 µl fresh E6 medium) on days 8 and 10. On day-12, in order to induce self-assembly of epidermis, all aggregates were transferred into individual wells of 24-well low-attachment plates (Thermo Scientific) in 500 µl organoid maturation medium (OMM) containing 1% Matrigel. To maintain the aggregates in a floating culture for constant medium circulation, 24-well plates were placed on an orbital shaker shaking at a speed of 65 rpm in the 37°C incubator with 5% CO2. OMM is composed of Advanced DMEM/F12 (Gibco) and Neurobasal (Gibco) media at a 1:1 ratio, 1X GlutaMax™ (Gibco), 0.5X B-27 Minus Vitamin A (Gibco), and 0.5X N2 (Gibco) supplements, 0.1 mM 2-Mercaptoethanol (Gibco), and 100 µg/ml Normocin. On differentiation day-15, half of the spent medium was replenished (removal of 250 µl of spent medium and addition of 250 µl fresh medium) with OMM containing 1% Matrigel. Starting from day-18, half-medium was changed every three days (from day-18 to day-30) or every other day (from day-30 to day-150 or longer) with fresh OMM without Matrigel.

tag: tissue

value: hESC-derived skin organoid

tag: hesc cell line

value: Day 85


title: scRNA_LCMV_Day7_CD4_CD8_NK_WT


title: MPRA, DNAvector4

city: London

first: James

middle: C

last: Lee

address: The Francis Crick Institute, 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

library_source: other

data_processing:
Quality control was performed using FastQC (v0.11.9)
Barcode counts were generated using a Python script - to be counted a sequenced barcode had to be a perfect match for an oligonucleotide library barcode and be followed by at least 10 bases of the expected constant sequence (XbaI restriction site and GFP).
To be deemed a successful transfection, at least 70% of the oligonucleotide library had to be represented in the resulting count file (i.e. count >1).
Raw count data was filtered to remove barcodes with a median counts per million (cpm) < 1 in either the mRNA or DNA samples.
Barcode counts for identical constructs were collapsed (summed) and quantile normalized (normalize.quantiles function in preprocessCore package in R version 4.1.0)
Assembly: hg19
Supplementary files format and content: barcode_counts.txt is a tab-delimited text file containing the raw barcode count data for every sample; normalised_collapsed_constructs.txt is a tab delimited text file containing the filtered, quantile-normalized and collapsed count data for unique genomic constructs tested in the MPRA

molecule: other

organism: synthetic construct

source_name: plasmid vector

growth_protocol: Monocytes were positively selected using CD14 Microbeads. Macrophage differentiation was performed using conditions that model chronic inflammation (TPP): 3 days GM-CSF (50ng/mL) followed by 3 days GM-CSF, TNFa (50ng/mL), PGE2 (1mg/mL), and Pam3CSK4 (1mg/mL). All cultures were performed at 37C, 5% CO2 in antibiotic-free RPMI1640 media containing 10% FBS, GlutaMAX, and MEM Non-Essential Amino Acids. On day 6 of culture, a minimum of 2x10^7 macrophages were harvested, counted, and nucleofected with the MPRA vector library (aliquots of 5x10^6 cells nucleofected with 5µg vector in 100 uL nucleofection buffer; Human Macrophage Nucleofection Kit, Lonza) using a Nucleofector 2b (Lonza, program Y-011).

extract_protocol:
Macrophages were detached using Accutase and were lysed. RNA was extracted from cell lysates using an AllPrep DNA/RNA Mini Kit (Qiagen).
Sequencing libraries were prepared by PCR (30 cycles) using PfuUltra II polymerase (Agilent) and custom primers that annealed to a site within EGFP (F) and the universal primer site in the oligonucleotide (R). Amplified libraries were cleaned using AMPure XP beads (Beckman Coulter): 0.6×, 1.6× and 1.0×. Four sequencing libraries were made from the input MPRA plasmid library (50ng vector, 18 PCR cycles). Libraries were sequenced in pools of 6.

value: plasmid vector

tag: replicate


title: Parasrampuria_shHD-33full_30lp

tag: cell line

tag: treatment

value: Transient transfection of smRNA encoding lentiviral plasmid


title: Parasrampuria_shHD-33full_UAC


title: Mini-colon CRC CM rep2

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

country: Spain

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

description: Mini-colon CRC CM rep2

data_processing:
Reads were aligned to the human genome (GRCh38) using star (version 2.7.0e).
R (version 4.1.2) was used to perform the differential expression analyses. Count values were imported and processed using edgeR.
Expression values were normalized using the trimmed mean of M values (TMM) method and lowly-expressed genes (< 1 counts per million) were filtered out.
Differentially expressed genes were identified using linear models (Limma-Voom), and P values were adjusted for multiple comparisons by applying the Benjamini-Hochberg correction method.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include count values for each sample

source_name: Primary CRC tumor

extract_protocol:
Cells were collected using TrypLE Express Enzyme, lysed in RLT buffer (QIAGEN, Catalog No. 74004), and the RNA was extracted using the QIAGEN RNeasy Micro Kit (QIAGEN, Catalog No. 74004) according to the manufacturer’s instructions.
Purified RNA was quality checked using a TapeStation 4200 (Agilent), and 60 ng were used for QuantSeq 3′ mRNA-Seq library construction according to the manufacturer’s instructions (Lexogen, Catalog No. 015.96).

value: Primary CRC tumor

value: colorectal cancer

value: CAF-conditioned medium


title: Parasrampuria_shHD-33full_nb


title: Parasrampuria_Round 1 NT

value: Transient transfection no treatment (NT) control


title: MPRA, DNAvector3


title: Mini-colon CRC CM rep3

description: Mini-colon CRC CM rep3


title: scRNA_LCMV_Day4_CD4_CD8_NK_KO

value: Spleen


title: MPRA, DNAvector2


title: scRNA_LCMV_Day4_CD4_CD8_NK_WT

value: CD4+CD8+NK cells


title: Mini-colon CRC CM rep1

description: Mini-colon CRC CM rep1


title: Parasrampuria_Round 2 NT


title: WT_M0_Rep2

value: bone marrow

value: macrophages

value: unstimulated


title: scRNA_KO_Spleen_AS15_Th1_Toxo_day7

source_name: Th1 cells

value: Th1 cells

value: in vivo


title: Parasrampuria_shHD-33full-mimic

value: HEK 293T

value: WT


title: Mini-colon CRC CAF rep3

description: Mini-colon CRC CAF rep3

value: CAF co-culture


title: MPRA, DNAvector1


title: S963Nr2: M-CSF HIF1α ko (Cre+) Control Rep2

value: LysMcre/+::HIF1{alpha}fl/fl (Cre+)

value: Bone marrow-derived macrophages

value: M-CSF (20ng/ml) for 6 days

value: untreated (control)


title: Day 85 DSP-GFP

value: hiPSC-derived skin organoid

value: DSP-GFP

value: Day 85


title: Exp#2_Bre1_RIP_GA813

city: Taiepi

first: Ming-Chia

address: Library, Info & Research Bldg, Rm 904 #155, Sec. 2, Li-Nong St

department: Department of Life Sciences and Institute of Genome Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
For Exp#1, sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using tophat (Bowtie2 [2.0.6.0] and Samtools [0.1.18.0]); For Exp#2, sequenced reads were trimmed for adaptor sequence, and mapped to dm6 whole genome using CLC Genomics Workbench 11.0.1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.
Assembly: dm6

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Oregon-R flies were raised under standard fly culture condition. For each RIP experiment, ~200 young females (12hr post eclosion) were collected for dissecting out oavries.

extract_protocol:
Collected ovaries were transferred into RIP buffer and then homogenized, lysed, and centrifuged to acquire ovarian lysate.
Library was prepared using iIlumina TruSeq RNA Sample Prep Kit v2 (Guide Revision F). The polyA selection steps were skipped, and samples were proceed directly to Fragmentation and Priming and cDNA synthesis.

treatment_protocol: Ovarian lysate collected from young females was spited into three parts for adding anti-IgG, anti-Lsd1 and anti-Bre1 antibody respectively.

value: Ovary

value: Oregon-R

value: wild type

tag: antibody


title: scRNA_KO_Spleen_Th1_Toxo_day7

value: Spleen

tag: cell type


title: Mini-colon CRC CAF rep2

description: Mini-colon CRC CAF rep2

value: Primary CRC tumor

value: colorectal cancer


title: Parasrampuria_shHD-33part 3'k

value: Transient transfection of smRNA encoding lentiviral plasmid


title: Mini-colon CRC CAF rep1

description: Mini-colon CRC CAF rep1


title: Exp#2_IgG_RIP_GA813

value: anti-IgG


title: scRNA_WT_Spleen_Th1_Toxo_day7

value: Th1 cells

value: in vivo


title: Parasrampuria_shHD1L-1d

value: HEK 293T

value: WT


title: Mini-colon CRC control rep3

description: Mini-colon CRC control rep3

value: No treatment (control)


title: FLC sample 8, tumor

first: Taran

last: Gujral

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

data_processing:
(1) For cell lines and tumors derived from human samples, sequencing data was aligned to human genome using STAR and raw counts were generated using Subread. (2) XenofilterR was applied to PDX tumor samples prior to above procedure to remove the mouse reads.
Assembly: GRCh38.p13
Supplementary files format and content: The processed files are in either csv or txt files and include the raw gene counts of expression data.

source_name: Tumor

extract_protocol:
Total RNA is extracted from the samples via Rneasy kit from Qiagen.
Library construction followed standard Novogene wokflow. Following cDNA synthesis, second-strand synthesis is initiated by adding second-strand synthesis buffer, deoxynucleotides, ribonuclease H, and DNA polymerase I. The process continues with terminal repair, A-ligation, and sequencing adaptor ligation. The double-stranded cDNA library is then completed through size selection and PCR enrichment.

value: Tumor


title: scRNA_KO_Pec_NK_Toxo_day7

source_name: NK cells

value: Peritoneal exudate

value: NK cells


title: Parasrampuria_shHD-33full


title: scRNA_WT_Pec_Th1_Toxo_day7


title: Parasrampuria_shHD1L-1b


title: Mini-colon CRC control rep2

description: Mini-colon CRC control rep2


title: Parasrampuria_shHD1L-1c


title: FLC sample 8, normal

source_name: Normal liver

value: Normal liver


title: FLC sample 7, tumor


title: TIG120_OSKLH_day5 (bulkRNA-seq)

city: San Francisco

first: Akira

last: Kunitomi

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description: Human dermal fibroblasts infected with SeV-OSKLH and sampled at day5

data_processing:
FASTQ files were generated from bcl files using bcl2fastq v2.17.1.14 (illumina) and processed using ENCODE long-rna-seq-pipeline v2.3.4.
Sequenced reads were mapped to the human reference genome (GRCh38) using TopHat 2.1.1 or STAR 2.5.1b with GENCODE v24 gene annotations.
Normalized gene expression data was calculated using RSEM 1.2.23.
Gene count data was obtained using featureCounts bundled in Subread 1.5.1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö+Y medium.

extract_protocol:
mRNA or total RNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human dermal fibroblasts

tag: gender

value: Female


title: TIG113_OSKLH_day5 (bulkRNA-seq)

source_name: Human dermal fibroblasts infected with SeV-OSKLH and sampled at day5


title: scRNA_WT_Pec_NK_Toxo_day7


title: Mini-colon CRC control rep1

description: Mini-colon CRC control rep1


title: FLC sample 6, tumor


title: scRNA_KO_Pec_Th1_Toxo_day7


title: FLC sample 7, normal


title: Parasrampuria_shHD1L-1a

tag: genotype


title: Parasrampuria_shHD1L-1


title: scRNA_KO_Spleen_Th1_Toxo_day3


title: FLC sample 6, normal


title: Exp#2_Lsd1_RIP_GA813

value: Ovary

value: Oregon-R

value: wild type


title: BJ_OSKLH_day5 (bulkRNA-seq)

value: Male


title: scRNA_WT_Spleen_AS15_Th1_Toxo_day7

value: Spleen


title: Parasrampuria_shHD-33part

value: Transient transfection of smRNA encoding lentiviral plasmid


title: scRNA_KO_Spleen_NK_Toxo_day3


title: TIG120_OSKL_day5 (bulkRNA-seq)

description: Human dermal fibroblasts infected with SeV-OSKL and sampled at day5


title: DSCL cases_4

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

institute: The University of Sheffield

data_processing:
Galaxy web platform, at usegalaxy.org version 1.9, was used for sample quality assessment, alignment, quantification and differential expression analysis.
Concatenate Datasets tool in Galaxy was used to combine the two fastq files for each sample and subsequent
Quality checks were carried out using the MultiQC tool that visually prsents a summary comparison of the output from numerous data across all samples
Using the HISAT2 tool, sample reads from the concatenated fastq files were mapped and aligned to the built-in reference human genome (Hg38).
Compact Idiosyncratic Gapped Alignment Report (CIGAR) was generated to pair the given sequences with their assigned position on the reference genome.
The QC statistics for aligned reads were calculated using samtools, enabling the flagging of any unmapped, unpaired, or duplicated PCR reads
Assembly: Hg38
Supplementary files format and content: Almansouri_Processed Data (samples1-12) - Excel sheet containing the processed count data for all 12 combined samples

source_name: Human post-mortem brain WM

extract_protocol:
CD68+ microglia were isolated from white matter groups (n=4 cases per group) from the Cognitive Function and Ageing Study neuropathology cohort by immuno-laser capture microdissection and total RNA was extracted from the LCM-isolated cells using the PicoPure RNA isolation kit (Life technologies: Applied Biosystems, USA).
8-μl of extracted total RNA was reversed transcribed to cDNA and amplified following 20 cycles of amplifying PCR (initial denaturation at 98°C for 45 s, the product was amplified at 98°C for 10 s, 62°C for 15 s, 72°C for 3 min, and then 72°C for 5 min). Following fragmentation, samples underwent adapter ligation and indexing to create cDNA libraries, permitting recognition of each sample once pooled. Each cDNA library product underwent amplification following 9 cycles of amplifying PCR (initial denaturation at 98°C for 30 s, then the product was amplified at 98°C for 10 s, 65°C for 75 s, and then 65°C for 5 min) and pooled. Pooled cDNA libraries were ran in duplicate lanes of a flow cell to maximize the number of mapped reads (100bp single read) and sequenced on an Illumina HiSeq 2500 platform using the Illumina TruSeq SBS Kit CA, United states).

value: Human post-mortem brain WM

value: Microglia


title: Parasrampuria_Round 4 shMCHR-33 full mimic

value: HEK 293T


title: DSCL cases_3


title: Parasrampuria_shHD1-1

value: WT


title: scRNA_WT_Spleen_Th1_Toxo_day3

value: Th1 cells

value: in vivo


title: scRNA_WT_Spleen_NK_Toxo_day3


title: TIG113_OSKL_day5 (bulkRNA-seq)

source_name: Human dermal fibroblasts infected with SeV-OSKL and sampled at day5


title: Parasrampuria_Round 2 shMCHR-33 full mimic


title: Parasrampuria_Round 1 shMCHR-33 full mimic


title: NAWM matched with the DSCL cases_4


title: scRNA_WT_Pec_Th1_Toxo_day3

value: Peritoneal exudate


title: Parasrampuria_Round 3 shMCHR-33 full mimic


title: DSCL cases_2


title: TIG120_OSKLH_day2 (bulkRNA-seq)

description: Human dermal fibroblasts infected with SeV-OSKLH and sampled at day2


title: Liver, normal IS dosage/H, 7

city: Shanghai

first: Yuan

last: Liu

address: No. 160 Dongchuan Rd.

institute: Renji Hospital

data_processing:
Cutadapt 4.4 was used to find and removes adapter sequences and low quality sequences
Hisat2 was applied for sequence mapping
StringTie was used for the assembly of RNA-Seq alignments into potential transcripts and Ballgown was used for FPKM calculation
Assembly: GRCh37
Supplementary files format and content: Excel file containing FPKM values for each sample

source_name: Liver

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) and enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). 1-2ug of RNA was used for library construction.
RNA library for RNA sequecing was prepared by KAPA Stranded RNA-Seq Library Prep Kit(Illumina)

value: Liver


title: scRNA_KO_Pec_Th1_Toxo_day3


title: scRNA_WT_Pec_NK_Toxo_day3

value: NK cells


title: TIG120_OSKL_day2 (bulkRNA-seq)

description: Human dermal fibroblasts infected with SeV-OSKL and sampled at day2

value: Human dermal fibroblasts


title: scRNA_KO_Pec_NK_Toxo_day3


title: DSCL cases_1


title: BJ_OSKLH_day2 (bulkRNA-seq)

source_name: Human dermal fibroblasts infected with SeV-OSKLH and sampled at day2


title: TIG113_OSKLH_day2 (bulkRNA-seq)

value: Female


title: Liver, normal IS dosage/H, 5


title: Liver, normal IS dosage/H, 6


title: NAWM matched with the DSCL cases_3


title: NAWM matched with the DSCL cases_2


title: bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_KO3

data_processing:
cDNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).
alignment: The run was demultiplexed and converted to FastQ using bcl2fastq v2.20.0.422 (Illumina) and mapped to mm10 using Tophat 2.1.0.
FPKM: Partek Genomics Suite 7.0 (Partek) was used to calculate Reads Per Kilobase of transcript, per Million mapped reads (RPKM), perform analysis of variance (ANOVA) comparisons, perform principal component analysis (PCA) and perform hierarchical clustering.
Assembly: mm10
Supplementary files format and content: excel files for bulk RNA-seq

extract_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by  washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10  ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Total RNA was extracted from 200,000 cells using QIAzol Lysis Reagent and the Direct-zol microprep RNA kit.
mRNA purification, cDNA synthesis and cDNA library preparation was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7770) and NEBNext Multiplex Oligos for Illumina (NEB, #E6609).

value: ex vivo


title: NAWM matched with the DSCL cases_1


title: Liver, normal IS dosage/H, 4


title: BJ_OSKL_day5 (bulkRNA-seq)


title: BJ_OSKL_day2 (bulkRNA-seq)

source_name: Human dermal fibroblasts infected with SeV-OSKL and sampled at day2


title: Liver, normal IS dosage/H, 3


title: Control WML _4


title: Control WML _3


title: bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_KO1


title: TIG120_OSKLH_day1 (bulkRNA-seq)

description: Human dermal fibroblasts infected with SeV-OSKLH and sampled at day1


title: Liver, normal IS dosage/H, 2


title: TIG113_OSKLH_day1 (bulkRNA-seq)

source_name: Human dermal fibroblasts infected with SeV-OSKLH and sampled at day1


title: Control WML _2


title: bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_WT2


title: bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_WT1


title: Liver, low IS dosage/L, 6


title: BJ_OSKLH_day1 (bulkRNA-seq)


title: Control WML_1


title: Liver, low IS dosage/L, 5


title: TIG120_OSKL_day1 (bulkRNA-seq)

description: Human dermal fibroblasts infected with SeV-OSKL and sampled at day1


title: 5637_siRNA_3

first: Sainab

last: Totonji

address: Breisacherstraße 66

institute: Uniklinik Freiburg

description:
5637_siRNA_6
Count_table_bladder_5637.txt

data_processing:
STAR
Trimmed sequence reads were mapped to hg19 using STAR (parameters --readFilesCommand gunzip -c --outSAMtype BAM SortedByCoordinate  --limitBAMsortRAM 60000000000)
Read count extraction and normalization were performed using homer(analyzeRepeats.pl and edgeR)
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

growth_protocol: RNA was extracted from 5637 and CAL-29 BC cell lines at day 3 after siRNA treatment.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). f total RNA was used for the construction of sequencing libraries.
RNA librairy was constructed at Novogene following standard protocols

value: Bladder cells

value: siRNA


title: Liver, low IS dosage/L, 7


title: bulkRNA_Th1_D3_Ifng(70)CTCFdel_F_KO2


title: 5637_siRNA_2

description:
5637_siRNA_5
Count_table_bladder_5637.txt


title: TIG113_OSKL_day2 (bulkRNA-seq)


title: TIG113_OSKL_day1 (bulkRNA-seq)

source_name: Human dermal fibroblasts infected with SeV-OSKL and sampled at day1


title: bulkRNA_Th1_D3_Ifng(70)CTCFdel_F_KO3


title: bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_KO2


title: BJ_OSKL_day1 (bulkRNA-seq)

value: Male


title: Liver, low IS dosage/L, 4


title: 5637_siRNA_1

description:
5637_siRNA_4
Count_table_bladder_5637.txt


title: Liver, normal IS dosage/H, 1


title: bulkRNA_Th1_D3_Ifng(70)CTCFdel_F_KO1

value: Spleen


title: bulkRNA_Th1_D7_Ifng(70)CTCFdel_F_WT3


title: TIG120 (bulkRNA-seq)

description: Human dermal fibroblasts

source_name: Human dermal fibroblasts


title: bulkRNA_Th1_D3_Ifng(70)CTCFdel_F_WT3


title: Liver, low IS dosage/L, 3


title: 5637_siCT_3

description:
5637_siCT_3
Count_table_bladder_5637.txt

value: siCT


title: Liver, low IS dosage/L, 2


title: 5637_siCT_2

description:
5637_siCT_2
Count_table_bladder_5637.txt


title: TIG113 (bulkRNA-seq)

description: Human dermal fibroblasts


title: bulkRNA_Th1_D3_Ifng(70)CTCFdel_F_WT2


title: 5637_siCT_1

description:
5637_siCT_1
Count_table_bladder_5637.txt


title: Liver, tolerant/T, 4


title: M993AAA_T1_scR_CEL-Seq2_4

first: Sander

description:
CelSeq-2
Pretreatment NBL M993AAA_T1

data_processing:
Failed reactions were identified by low levels of ERCC external RNA controls and excluded. Furthermore, a liveness threshold was calculated for each plate based on the wells with no cell added, in order to distinguish live cells from dead and/or apoptotic cells. This threshold was set to a minimum of 500 transcripts.
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: NBL tumor lymph node left inguinal

extract_protocol:
Tumor material was collected in the operating room by Truecut biopsy (samples at diagnosis) or surgical resection (debulking procedure after induction chemotherapy). The Dutch samples were gently dissociated into single‐cells and sorted by flow cytometry for single‐cell RNA sequencing using the CEL‐Seq2 platform. In brief, preparation of the tumor pieces for single‐cell RNA sequencing was started within 4 hours after the surgery. The material was minced into pieces <1mm3 and dissolved by enzymatic digestion with collagenase I, II and IV (2.5 mg/mL) at 37°C with agitation for max. 1 hour. The samples were filtered through a 70 μm cell strainer and washed in DMEM. Cells were further separated into a single cell suspension with the NeuroCult dissociation kit according to the manufacturer's protocol (StemcellTM Technologies, cat#05707), washed and stained with DAPI and DRAQ5. Next to this unbiased strategy, some samples were additionally stained with antibodies to enrich for T cell populations (NB124, NB125 with CD3‐PE (Biolegend, cat#300308); NB124 with TCRγδ‐BV421 (Biolegend, cat#331217) or with GD2‐FITC (BD Biosciences, cat#563439) to enrich for tumor cells (000GGU, 000GXF, NB106, NB107, NB098, NB125, NB125, NB130, NB152). Single live cells were sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a FACSJazz, FACSAria II or Sony SH800S machine and subsequently spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing. Peripheral blood mononuclear cells (PBMC) from 5 healthy young adult donors (mean age 28) were isolated by Ficoll-Paque (VWR) density centrifugation and stained with fixable viability dye efluor506 (eBioscience, cat#65‐0866‐14), CD3‐PE (Biolegend, cat#300308) and CD56‐APC (Biolegend, cat#318310) antibodies. Subsequently, live CD3+ T cells and CD56+ NK cells were FACS sorted into 384‐well plates containing 10 μl of mineral oil, 50 nl of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike‐Ins on a Sony SH800S machine. The plates were spun down, snap‐frozen on dry ice, and stored in ‐80⁰C to proceed with the total transcriptome amplification, library preparation and sequencing.
All samples were processed for total transcriptome amplification, library preparation and sequencing into Illumina sequencing libraries as previously described70. Paired‐end 2x75 bp sequencing read length was used to sequence the prepared libraries using the Illumina NextSeq sequencer. Sharq preprocessing and QC pipeline were applied to process the single‐cell RNA‐seq data as described71. Read mapping was done using STAR version 2.6.1 (RRID:SCR_004463) on the hg38 Patch 10 human genome. Function featureCounts (RRID:SCR_012919) of the subread package (version 1.5.2) was used to assign reads based on GENCODE version 26 (RRID:SCR_014966).

value: NBL tumor lymph node left inguinal

tag: tumor type

value: High-risk NBL

tag: tumor stage

value: pre-treatment

tag: Sex

value: female

value: MYCN amplified


title: bulkRNA_Th1_D3_Ifng(70)CTCFdel_F_WT1


title: Liver, low IS dosage/L, 1


title: popliteal, males from uninfected mothers, rep1, V(D)J-derived cDNA

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

description:
UNINF_Male_VDJ
V(D)J/BCR

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x Genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: 10x Genomics output files.
Supplementary files format and content: filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Female_GEX_filtered_feature_bc_matrix-2.h5: mRNA/transcript of germinal center B cells.
Supplementary files format and content: INF_Female_SP_filtered_feature_bc_matrix.h5: Surface protein information.
Supplementary files format and content: INF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: INF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Female_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Library strategy: V(D)J

source_name: Popliteal lymph node

extract_protocol:
The popliteal lymph node of mice born from S. mansoni infected mothers or control mothers were harvested 14 days after footpad immunization with 1.10th the dose of a commercial Tetanus/Diphtheria vaccine. Lymph nodes were smashed through a 70um filter to form a single cell suspension and washed before pelleting and staining. Primary antibody staining was done for 30 minutes in the dark at 4 degrees and washed twice before cell sorting on a FACS Aria. After sorting, cells were stained with FITC-conjugated Tetanus Toxoid for 15 minutes and then the anti-FITC TotalSeq antibody per manufacturer's instruction. Cells were counted and resuspended at a concentration of 10,000 cells/ul before proceeding to library construction.
Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and amplified by PCR according to the Chromium Single Cell 5’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. For all cDNA library preparations, we further proceeded according to the manufacturer’s instructions for Single Cell 5’ v2 protocol (10x Genomics). mRNA and ADT sequences were combined in Cell Ranger, outputting one file per sample for those two libraries.
V(D)J library: Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics).
CITEseq library: Library was prepared using Chromium Single Cell 5ʹ v2 protocol (10x Genomics).

value: Popliteal lymph node

value: Germinal Center B cells

tag: condition

value: Born to uninfected (control) mothers


title: popliteal, males from uninfected mothers, rep1, ADT-derived cDNA

description:
UNINF_Male_SP
protein

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x Genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: 10x Genomics output files.
Supplementary files format and content: filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Female_GEX_filtered_feature_bc_matrix-2.h5: mRNA/transcript of germinal center B cells.
Supplementary files format and content: INF_Female_SP_filtered_feature_bc_matrix.h5: Surface protein information.
Supplementary files format and content: INF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: INF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Female_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Library strategy: CITE-seq

tag: antibodies/tags

value: TotalSeq-C0988 anti-FITC Antibody


title: Cal29_siRNA_3

description:
Cal29_siRNA_6
Count_table_bladder_Cal29.txt

value: WT


title: Cal29_siRNA_1

description:
Cal29_siRNA_4
Count_table_bladder_Cal29.txt


title: M993AAA_T1_scR_CEL-Seq2_2

description:
CelSeq-2
Pretreatment NBL M993AAA_T1


title: Liver, tolerant/T, 2

value: Liver


title: Cal29_siRNA_2

description:
Cal29_siRNA_5
Count_table_bladder_Cal29.txt


title: Liver, tolerant/T, 3


title: popliteal, males from uninfected mothers, rep1, mRNA-derived cDNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, V(D)J and ADT) was performed using the 10x Genomics Cell Ranger pipeline where ADT and V(D)J sequences were treated as Custom library with default settings (v5.0.0) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.1.0 (cell and gene filtering, clustering, differential gene expression analysis) for mRNA and ADT. V(D)J was processed using scRepertoire.
Assembly: mm10-3.0.0
Supplementary files format and content: filtered_feature_bc_matrix.h5: 10x Genomics output files.
Supplementary files format and content: filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Female_GEX_filtered_feature_bc_matrix-2.h5: mRNA/transcript of germinal center B cells.
Supplementary files format and content: INF_Female_SP_filtered_feature_bc_matrix.h5: Surface protein information.
Supplementary files format and content: INF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: INF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: INF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Female_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Female_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.
Supplementary files format and content: UNINF_Male_GEX_filtered_feature_bc_matrix.h5: Processed GEX and SP were combined into one file in cell ranger.
Supplementary files format and content: UNINF_Male_VDJ_filtered_contig_annotations.csv: V(D)J sequences of germinal center B cells.


title: M993AAA_T1_scR_CEL-Seq2_1

description:
CelSeq-2
Pretreatment NBL M993AAA_T1


title: M993AAA_T1_scR_CEL-Seq2

description:
CelSeq-2
Pretreatment NBL M993AAA_T1


title: Cal29_siCT_3

description:
Cal29_siCT_3
Count_table_bladder_Cal29.txt


title: popliteal, females from uninfected mothers, rep1, V(D)J-derived cDNA

description:
UNINF_Female_VDJ
V(D)J/BCR

value: Female


title: Cal29_siCT_2

description:
Cal29_siCT_2
Count_table_bladder_Cal29.txt

value: Bladder cells


title: FnEV_2

city: Chengdu

first: Xin

last: Zheng

state: Sichuan

address: No. 14, Section 3, Renmin South Road

institute: Sichuan University

data_processing:
The raw paired-end reads were trimmed, and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the fragments per kilobase million (FPKM) method.
Differential expression genes (DEG) analysis was performed using the DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: Matrix table with FPKM for every gene and every sample.
Supplementary files format and content: only one processed data file

growth_protocol: Cells were routinely cultured in Dulbecco's modified Eagle medium (DMEM; Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (FBS) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA were extracted and purified using MiniBest Universal RNA Extraction kit (Takara, Japan) according to the manufacturer’s instruction.
The cDNA library was prepared following the procedures of TruSeqTM RNA sample preparation kit (Illumina, San Diego, CA) using 1μg total RNA

treatment_protocol: The cells cultured were grown to ~90% confluency, followed by treatemnt of 5 μg/mL FnEVs or PBS for 2 hr at 37°C in a humidified 5% CO2 atmosphere.

value: FnEV


title: FnEV_3


title: popliteal, females from uninfected mothers, rep1, ADT-derived cDNA

description:
UNINF_Female_SP
protein


title: BJ (bulkRNA-seq)

description: Human dermal fibroblasts

value: Human dermal fibroblasts

value: Male


title: popliteal, females from uninfected mothers, rep1, mRNA-derived cDNA


title: FnEV_1


title: M993AAA_T1_scR_CEL-Seq2_3

description:
CelSeq-2
Pretreatment NBL M993AAA_T1


title: M787AAA_T2_scR_CEL-Seq2_2

description:
CelSeq-2
Pretreatment NBL M787AAA_T2

source_name: NBL tumor left adrenal gland

value: NBL tumor left adrenal gland

value: CDK4 amplified


title: popliteal, males from infected mothers, rep1, V(D)J-derived cDNA

description:
INF_Male_VDJ
V(D)J/BCR

value: Born to S. mansoni infected mothers


title: M787AAA_T2_scR_CEL-Seq2_1

description:
CelSeq-2
Pretreatment NBL M787AAA_T2

value: High-risk NBL

value: pre-treatment